BCHM 4116 1st Edition Exam 3 Study Guide Lectures 22 31 Chapter 29 Transcription and Regulation of Gene Expression 1 29 1 Genes Transcribed in Prokaryotes a RNA pol i 2 ii 2 large subunits 1 performs most of enzymatic function iii Binding of subunit recognizes diff DNA sequences that act as promoters 1 Promoters identify transcription start site b Transcription has 4 stages i Binding of RNA pol at promter site 1 subunit recognizes promoter sequence RNA pol promter form a complex 2 3 AKA closed promoter complex b c dsDNA is not opened 4 1 transcription start site 5 within promoter are 2 consensus sequences a Pribnow box 10 region i TATAAT b 35 region 6 subunit recognizes and binds to 10 35 regions ii Initiation of polymerization 1 RNA pol does not require primer 2 subunit dissociates from RNA pol once 9 12 resides long has been formed completion of initiation 3 core RNA pol highly processive and goes on to synthesize remainder of mRNA iii Chain elongation 1 Catalyzed by core polymerase 2 To prevent torsional stress from inhibiting transcription gyrase introduces negative supercoils thereby remove positive supercoils ahead of RNA pol 3 Topoisomerase removes negative supercoil behind DNA iv Chain termination 1 Bacteria a Intrinsic termination i Specific sequences in DNA called termination sites 1 Inverted repeats typically G C rich so forms stem loop structure 2 Nonrepeating segment that punctuates inverted repeats 3 6 8 A s in DNA coding for U s in transcript b Rho factor i Less common mechanistically more complex ii ATP dependent hexameric helicase iii Catalyzes unwinding of RNA DNA duplex iv Rho factor recognizes and binds to C rich region then advances in 5 3 direction until reaches transcription bubble v There it catalyzes unwinding of transcript and template releasing RNA chain 2 Regulation of Transcription in Prokaryotes a Operator regulatory sequence lying adjacent to DNA being transcribed determines whether transcription takes place b Operons transcriptional control regions a set of related structural genes all organized in a contiguous linear array along chromosome i Expression of operon is determined by access of RNA pol to promoter and occupancy of operation by regulatory proteins influences this access ii Induction activates transcription from promoter repression prevents it c Attenuation regulates transcription after it has begun i Any regulation mechanism that manipulates transcription termination or transcription pausing to regulate gene transcription downstream 3 29 3 Gene Transcription in Eukaryotes a DNA of eukaryotes is wrapped around histones forming nucleosomes b Nucleosomes repress gene expression c Nucleosomes control gene expression by controlling transcriptional apparatus i 2 classes of transcriptional co regulators necessary to overcome nucleosome repression 1 Enzymes that covalently modify nucleosome histone proteins to loosen histone DNA interactions 2 ATP dependent chromatin remodeling complexes d Transcription in Eukaryotes e The three classes of RNA polymerase in eukaryotes RNA polymerases I II and III i RNA pol I localized to nucleolus transcribes rRNA ii RNA pol II transcribes protein encoding genes mRNA iii RNA pol III transcribes tRNA genes rRNA genes other small RNAs iv ALL 3 RNA pol interact w their promoters via transcription factors 1 Transcription factors DNA binding proteins that recognize accurately initiate transcription at specific promoter sequences f The structure and function of RNA polymerase II the mRNAsynthesizing RNA polymerase i CTD is essential to RNA pol II function ii Only RNA pol II whose CTD is not phosphorylated can initiate transcription 1 But phosphorylation transcription elongation 2 Phosphorylation triggers conversion of an initiation complex into an elongation complex g Transcription regulation in eukaryotes including i General features of gene regulatory sequences promoters enhancers and response elements 1 Promoters consist of 2 features a Core element near transcription start site where general transcription factors bind b Regulatory elements 2 Enhancers assist initiation a Location of enhancers relative to transcription start site is not fixed i May be thousand nucleotides away from promoter ii Act to enhance transcription even if positioned downstream b BIDIRECTIONAL in that they function in either orientation c promiscuous b c they stimulate transcription from an promoter that happens to be in their vicinity d enhancer function is dependent on recognition by a specific transcription factor 3 Response Elements promoter responsive to common regulation a Ex heat shock element HSE b Glucocorticoid response element GRE c Found in promoter region ii Transcription initiation by RNA pol II requires TBP and GTFs 1 The general transcription factors GTFs a GTFs TFIIA TFIIB TFIID TFIIF TFIIH TFIIS b TFIID TBP c TFIIA stabilizes TFIID and TATA box d TFIIB recruits preinitiation complex PIC to promoter positioning RNA pol active site over promoter e TFIIE TFIIF enhance promoter PIC interaction f TFIIH helicase aids in creating transcription bubble 2 Mediators a Bridge b w enhancers transcription coactivators to RNA pol at the promoter b Ultimate regulator of transcription c Acts as repressor and activator of transcription 3 Alleviating the repression due to nucleosomes a Relief from repression imposed by chromatin structure requires factors that can reorganize chromatin alter nucleosomes so that promoters become accessible to transcriptional machinery i Chromatin remodeling complexes 1 Mediate ATP dependent conformational noncovalent changes in nucleosome structures 2 Nucleic acid stimulated multisubunit ATPase ii Histone modifying enezymes 1 Introduce covalent modifications into N terminal tails of histone a 1 Diminish DNA histone associations via disruption of electrostatic interactions b 2 Introduce subsititutaions that can recruit binding of new protein participants through protein protein interactions b Histone acetyl transferases HATs i Acetylation of amino group on lysine residues in histone tails ii N acetylation suppresses positive charge in histone tails diminishing their interaction w negatively charged DNA c Transcription regulation i Phosphorylation of Ser residues ii Methylation of Lys residues h A general model for eukaryotic gene activation based on the preceding 4 29 5 Eukaryotic Transcripts Processed and Delivered to Ribosome for Translation a Transcription occurs on DNA in nucleus and translation occurs on